ROntoTools: R Onto-Tools suite

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Suite of tools for functional analysis.

Author
Calin Voichita <calin@wayne.edu> and Sahar Ansari <saharansari@wayne.edu> and Sorin Draghici <sorin@wayne.edu>
Date of publication
None
Maintainer
Calin Voichita <calin@wayne.edu>
License
CC BY-NC-ND 4.0 + file LICENSE
Version
2.2.0

View on Bioconductor

Man pages

alpha1MR
Compute alpha weights
alphaMLG
Compute alpha weights
compute.fisher
Combine independent p-values using the Fisher method
compute.normalInv
Combine independent p-values using the normal inversion...
KEGGpathway2Graph
Modified version of the same function from KEGGgraph
keggPathwayGraphs
Download and parse KEGG pathway data
keggPathwayNames
Obtain KEGG pathway titles
nodeWeights
Retrieve the node weights of a graph
pDis
Primary dis-regulation: Pathway analysis approach based on...
pDisPathway-class
Class that encodes the result of pDis analysis for a single...
pDisRes-class
Primary dis-regulation (pDis) result class
pe
Pathway-Express: Pathway analysis of signaling pathways
peEdgeRenderInfo
Extract edge render information from a 'pePathway-class'...
peNodeRenderInfo
Extract node render information from a 'pePathway-class'...
pePathway-class
Class that encodes the result of Pathway-Express for a single...
peRes-class
Pathway-Express result class
plot.pePathway-methods
Plot pathway level statistics
plot.peRes-methods
Plot Pathway-Express result
setEdgeWeights
Set gene weights based on edge type
setNodeWeights
Set node weights
subGraphByNodeType
Modified version of the same function from KEGGgraph
summary.pDisRes
Summarize the results of a primary dis-regulation (pDis)...
Summary-pDisRes-method
Summarize the results of a Pathway-Express analysis
summary.peRes
Summarize the results of a Pathway-Express analysis
Summary-peRes-method
Summarize the results of a Pathway-Express analysis

Files in this package

ROntoTools/DESCRIPTION
ROntoTools/LICENSE
ROntoTools/NAMESPACE
ROntoTools/NEWS
ROntoTools/R
ROntoTools/R/AllClasses.R
ROntoTools/R/AllGenerics.R
ROntoTools/R/Summary-methods.R
ROntoTools/R/graphWeights.R
ROntoTools/R/keggDataREST.R
ROntoTools/R/nodeWeights-methods.R
ROntoTools/R/pDisExpress.R
ROntoTools/R/pDisPathway-utils.R
ROntoTools/R/pathwayExpress.R
ROntoTools/R/pePathway-utils.R
ROntoTools/R/plot-methods.R
ROntoTools/R/renderInfo-methods.R
ROntoTools/R/summary.pDisRes.R
ROntoTools/R/summary.peRes.R
ROntoTools/R/utils.R
ROntoTools/build
ROntoTools/build/vignette.rds
ROntoTools/inst
ROntoTools/inst/doc
ROntoTools/inst/doc/rontotools.R
ROntoTools/inst/doc/rontotools.Rnw
ROntoTools/inst/doc/rontotools.pdf
ROntoTools/inst/extdata
ROntoTools/inst/extdata/E-GEOD-21942.topTable.RData
ROntoTools/inst/extdata/KEGGRESTunparsed_hsa.RData
ROntoTools/inst/extdata/kpgDefault.RData
ROntoTools/inst/unitTests
ROntoTools/inst/unitTests/test_alpha.R
ROntoTools/inst/unitTests/test_graphWeights.R
ROntoTools/inst/unitTests/test_nodeWeights.R
ROntoTools/inst/unitTests/test_pe.R
ROntoTools/man
ROntoTools/man/KEGGpathway2Graph.Rd
ROntoTools/man/Summary-pDisRes-method.Rd
ROntoTools/man/Summary-peRes-method.Rd
ROntoTools/man/alpha1MR.Rd
ROntoTools/man/alphaMLG.Rd
ROntoTools/man/compute.fisher.Rd
ROntoTools/man/compute.normalInv.Rd
ROntoTools/man/keggPathwayGraphs.Rd
ROntoTools/man/keggPathwayNames.Rd
ROntoTools/man/nodeWeights.Rd
ROntoTools/man/pDis.Rd
ROntoTools/man/pDisPathway-class.Rd
ROntoTools/man/pDisRes-class.Rd
ROntoTools/man/pe.Rd
ROntoTools/man/peEdgeRenderInfo.Rd
ROntoTools/man/peNodeRenderInfo.Rd
ROntoTools/man/pePathway-class.Rd
ROntoTools/man/peRes-class.Rd
ROntoTools/man/plot.pePathway-methods.Rd
ROntoTools/man/plot.peRes-methods.Rd
ROntoTools/man/setEdgeWeights.Rd
ROntoTools/man/setNodeWeights.Rd
ROntoTools/man/subGraphByNodeType.Rd
ROntoTools/man/summary.pDisRes.Rd
ROntoTools/man/summary.peRes.Rd
ROntoTools/tests
ROntoTools/tests/runTests.R
ROntoTools/vignettes
ROntoTools/vignettes/rontotools.Rnw
ROntoTools/vignettes/rontotools.bib